4f0x

Crystal structure of human Malonyl-CoA Decarboxylase (Peroxisomal Isoform)

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Malonyl-CoA decarboxylase, mitochondrial

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	N~3~-[(2R)-2-hydroxy-4-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}-3,3-dimethylbutanoyl]-beta-alaninamide × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	N~3~-[(2R)-2-hydroxy-4-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}-3,3-dimethylbutanoyl]-beta-alaninamide × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DCMC_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–458； UniProt 39–493 Author chain B； PDBConstruct 4–458； UniProt 39–493 Author chain C； PDBConstruct 4–458； UniProt 39–493 Author chain D； PDBConstruct 4–458； UniProt 39–493 Author chain E； PDBConstruct 4–458； UniProt 39–493 Author chain F； PDBConstruct 4–458； UniProt 39–493 Author chain G； PDBConstruct 4–458； UniProt 39–493 Author chain H； PDBConstruct 4–458； UniProt 39–493

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4f0x
Deposition date deposition_date	2012-05-05
Structure title title	Crystal structure of human Malonyl-CoA Decarboxylase (Peroxisomal Isoform)
Keywords keywords	Enzyme, Peroxisome, LYASE; LYASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

4f0x__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4f0x__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4f0x__assembly_2__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	43.89 Å
Rg (electron density)	43.40 Å
Total Rg	43.76 Å
Atom count	14017
Residues	1776
Excluded volume	250050 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4f0x__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4f0x__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Malonyl-CoA decarboxylase, mitochondrial
Molecular weight formula_weight	51281.7 kDa
EC 编号 ec_number	4.1.1.9
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	28107

GSGAMDELLRRAVPPTPAYELREKTPAPAEGQCADFVSFYGGLAETAQRAELLGRLARGFGVDHGQVAEQSAGVLHLRQQQREAAVLLQAEDRLRYALVPRYRGLFHHISKLDGGVRFLVQLRADLLEAQALKLVEGPDVREMNGVLKGMLSEWFSSGFLNLERVTWHSPCEVLQKISEAEAVHPVKNWMDMKRRVGPYRRCYFFSHCSTPGEPLVVLHVALTGDISSNIQAIVKEHPPSETEEKNKITAAIFYSISLTQQGLQGVELGTFLIKRVVKELQREFPHLGVFSSLSPIPGFTKWLLGLLNSQTKEHGRNELFTDSECKEISEITGGPINETLKLLLSSSEWVQSEKLVRALQTPLMRLCAWYLYGEKHRGYALNPVANFHLQNGAVLWRINWMADVSLRGITGSCGLMANYRYFLEETGPNSTSYLGSKIIKASEQVLSLVAQFQKNSKL

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	N~3~-[(2R)-2-hydroxy-4-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}-3,3-dimethylbutanoyl]-beta-alaninamide
Molecular weight formula_weight	378.2 kDa
Source method src_method	syn
Copy count entity_count	4

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6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id	4f0xA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	90 — Malonyl-CoA decarboxylase, oligemerization domain

Domain ID domain_id	4f0xA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	150 — Malonyl-CoA decarboxylase, catalytic domain

Domain ID domain_id	4f0xB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	90 — Malonyl-CoA decarboxylase, oligemerization domain

Domain ID domain_id	4f0xB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	150 — Malonyl-CoA decarboxylase, catalytic domain

Domain ID domain_id	4f0xC01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	90 — Malonyl-CoA decarboxylase, oligemerization domain

Domain ID domain_id	4f0xC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	150 — Malonyl-CoA decarboxylase, catalytic domain

Domain ID domain_id	4f0xD01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	90 — Malonyl-CoA decarboxylase, oligemerization domain

Domain ID domain_id	4f0xD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	150 — Malonyl-CoA decarboxylase, catalytic domain

Domain ID domain_id	4f0xE01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	90 — Malonyl-CoA decarboxylase, oligemerization domain

Domain ID domain_id	4f0xE02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	150 — Malonyl-CoA decarboxylase, catalytic domain

Domain ID domain_id	4f0xF01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	90 — Malonyl-CoA decarboxylase, oligemerization domain

Domain ID domain_id	4f0xF02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	150 — Malonyl-CoA decarboxylase, catalytic domain

Domain ID domain_id	4f0xG01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	90 — Malonyl-CoA decarboxylase, oligemerization domain

Domain ID domain_id	4f0xG02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	150 — Malonyl-CoA decarboxylase, catalytic domain

Domain ID domain_id	4f0xH01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	90 — Malonyl-CoA decarboxylase, oligemerization domain

Domain ID domain_id	4f0xH02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	150 — Malonyl-CoA decarboxylase, catalytic domain

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Unit-cell length a length_a	80.420 Å
Unit-cell length b length_b	103.310 Å
Unit-cell length c length_c	134.240 Å
Unit-cell angle α angle_alpha	95.32 °
Unit-cell angle β angle_beta	90.22 °
Unit-cell angle γ angle_gamma	94.46 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.290 Å
Low-resolution limit resolution_low	66.800 Å
R factor r_factor	0.2456
R_work r_work	0.2445
R_free r_free	0.2667

Crystal structure of human Malonyl-CoA Decarboxylase (Peroxisomal Isoform)

1. Protein Identity and Related Structures Protein Identity & Related Structures

Malonyl-CoA decarboxylase, mitochondrial

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4f0x__assembly_2__model_1

4f0x__assembly_2__model_1 | I(q)

4f0x__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)

Crystal structure of human Malonyl-CoA Decarboxylase (Peroxisomal Isoform)

1. Protein Identity and Related Structures Protein Identity & Related Structures

Malonyl-CoA decarboxylase, mitochondrial

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4f0x__assembly_2__model_1

4f0x__assembly_2__model_1 | I(q)

4f0x__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)